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 Forum index » Advanced Topics » Additional Software (PETs, n' stuff) » REQUESTS
Request: SciPlore 15 beta [FILLED]
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Puppyt

Joined: 09 May 2008
Posts: 568
Location: Gatton, Queensland

PostPosted: Fri 06 May 2011, 06:04    Post subject:  Request: SciPlore 15 beta [FILLED]
Subject description: Mind-mapping, pdf management, bibliography tool, Freemind Scholar
 

About a year ago, robwoj44 very kindly provided a pet for SciPlore 10 beta - formerly known as "FreeMind Scholar", a software package that combined mind-mapping with pdf management AND bibliography creation for students and researchers alike (http://www.murga-linux.com/puppy/viewtopic.php?t=57307).

The pet hasn't been updated with all the improvements listed here http://www.sciplore.org/software/sciplore_mindmapping/#download, and I am requesting that someone please accept the challenge to develop an updated pet or sfs for the Puppy community. (And me, plus a bunch of uni students I hope to lure off Vista and Win7...)

I unfortunately have problems with robwoj44's earlier pet as it failed to integrate fully with PDF and image files in a way I outlined in my original request here:http://www.murga-linux.com/puppy/viewtopic.php?t=56136. I wonder whether these problems I encountered remain Puppy-specific, or have been solved in the later upgrades of SciPlore.

Thanks very much for your attention,

Puppyt


UPDATE: THREAD SUMMARY 2Aug '11
I think I can safely call this request "FILLED".
Many Thanks to Geoffrey and Ariel for their impetus to get this over the line. SciPlore (FreeMind Scholar) is just about to evolve into FreePlane-based "Docear" that hopefully won't encounter the XDG-open problem in Puppy. SciPlore in Puppy however will still require some manual massage to have it working to the user's requirements. Here's the copy of my openfile.sh:

Code:

#!/bin/bash
#this script opens files within freemind-0.9.0
#to use install the script in /usr/bin
#open freemind and go to Tools>Preferences>HTML menu
#in Defaul Browser Command Other Os, insert this command: openfile.sh {0}
#save
#quit freemind and launch it again
#
#you can add other programs provided you add the extension of the file you want to launch (last 3 characters)



ext=`echo "$@" | sed 's/.*\(...\)$/\1/'`

if [ "$ext" == doc ] ; then abiword "$@"
   elif [ "$ext" == txt ] ; then abiword "$@"
   elif [ "$ext" == tml ] ; then firefox "$@"
   elif [ "$ext" == abw ] ; then abiword "$@"
   elif [ "$ext" == pdf ] || [ "$ext" == PDF ] ; then evince "$@"
   # elif [ "$ext" == pdf ] || [ "$ext" == PDF ] ; then FoxitReader "$@"
   elif [ "$ext" == jpg ] || [ "$ext" == JPG ] ; then viewnior "$@"
   # elif [ "$ext" == jpg ] || [ "$ext" == JPG ] ; then evince "$@"

fi

I've commented out the jpg option for eVince - it can read a wide range of file formats - and it works here as does Viewnior. It also opens PDF's correctly and very rapidly. I would prefer Foxit Reader as apparently SciPlore retains user's highlighting and annotations made to any pdf in Foxit Reader. In my findings it just starts Foxit, doesn't open the pdf, and hence is commented out here. I'll post any other problem I might find in the next few days of use.
Very Happy

[Test environment: using pemasu's Polarpup-003, Woof, kernel 2.6.39-3(i686); Geoffrey's SciPlore 15beta pet; Ariel's openfile and cgj-jre-4-4-4-3-lucid pets (latter might not be required), with this added to my etc/profile file:
Code:
export JAVA_HOME=/usr/lib/jvm/java-6-openjdk
export PATH=$PATH:/usr/lib/jvm/java-6-openjdk/jre/bin

Plus, ttuuxx's jre-6u26-1-i386 and evince-2.30.3-i386 pets; and the FoxitReader-1.1-lucid pet downloaded via PPM]

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Last edited by Puppyt on Wed 03 Aug 2011, 22:15; edited 2 times in total
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Geoffrey


Joined: 30 May 2010
Posts: 1478
Location: Queensland Australia ɹǝpu∩uʍop

PostPosted: Fri 06 May 2011, 23:17    Post subject:  

I posted a download for it here, hope it's what you want.
http://www.murga-linux.com/puppy/viewtopic.php?t=57307
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Puppyt

Joined: 09 May 2008
Posts: 568
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PostPosted: Fri 06 May 2011, 23:31    Post subject:  

WOW!
Thanks Geoffrey - (and you're only an Aussie stones-throw away) I'll test this in Lucid puplets with great interest indeed - this is fabulous,
Cheers!

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Geoffrey


Joined: 30 May 2010
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Location: Queensland Australia ɹǝpu∩uʍop

PostPosted: Sat 07 May 2011, 00:10    Post subject:  

Puppyt wrote:
WOW!
Thanks Geoffrey - (and you're only an Aussie stones-throw away) I'll test this in Lucid puplets with great interest indeed - this is fabulous,
Cheers!


No worries mate,

if you need a sfs of it let me know, it will be "SciPlore_MindMapping_Linux-015b_525.sfs" and I'll upload it for you.

I'm sure others would like to give it a try, it looks interesting, wonder what is does, Confused lol

Geoffrey

PS if you want it in a different menu just state which one, I just thought docs was the appropriate place
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Puppyt

Joined: 09 May 2008
Posts: 568
Location: Gatton, Queensland

PostPosted: Sat 07 May 2011, 05:00    Post subject:
Subject description: Integrating SciPlore with Puppy 5
 

Cheers Geoffrey -
I've loaded your pet into a frugal-install Lucid 5.20 experimental project I have going on my desktop (2.6.33.2 (i686) kernel, 2.4GHz Celeron, 2Gb RAM). I have CowLog1.1 deb, KDE3.5, Kommander, R+Rcmdr, Java 1.6.0_22 all working happily here but importantly for SciPlore integration: AbiWord 2.8.6, Viewnoir 1.0, mpaint 3.34.59, and ePDFView 0.1.7. So I think that my foundations are basically sound (well - not mine, but you know what I mean).
Unfortunately SciPlore15 still gives me the same problems as I encountered with robwoj44's version, as I outlined earlier. With a *little* more Puppy/Linux experience under my belt I've had a bit of a brainstorm into fixing the possible problem with SciPlore's integration with Puppy. Here's the behaviour:-
1) I can drag all types of documents (doc, rtf, jpg, pdf) straight onto wherever I like to create mindmap structures that are completely editable (i.e., move and attribute details to "nodes" - data and/or links to files) just as the SciPlore developers intended.
2) I can create a "monitored folder" containing a library of PDF files from within SciPlore - ALL the bookmarks/subheadings to ALL the files available are generated swiftly and clearly displayed in an automatically-generated map. Badda-bing, badda-boom - worth the price of admission.
3) I haven't tried generating BibTex keys as I haven't got SciPlore's modified JabRef for extracting PDF metadata - baby steps first...
4) Click on the mindmap nodes with DOC or RTF files linked to them, and AbiWord opens those files nearly instantaneously. Wheee!

Here's where I get 'fails":
5) Click on an image file (jpg) and mtPaint baulks at opening the file correctly ("Cannot open file" error message) from WITHIN SciPlore - even though the file can be dragged from ROX into mtPaint and open correctly from outside SciPlore,
and;
6) Click on a PDF file and ePDFViewer gives me an "Encrypted Document: This document is encrypted and can't be accessed. Please enter the document's password:". The document is not actually encrypted and opens fine from outside SciPlore.

So where I think there is a problem is with SciPlore's automatic attribution of file types and applications on installation. Maybe ePDFView has inherent problems in Puppy 5 (?) and if I point SciPlore to another app like evince2, PDFedit etc I might have the files accessed properly from within SciPlore. Same with a re-directed image app instead of mtPaint, perhaps. Trouble is, I don't know if this is the solution, even if I had the nous to find out where to make the changes.
Any suggestions from any Puppians to solving this problem gratefully received,
Cheers!

PS Actually Geoffrey, I think that having SciPlore within the 'Document/Publishing' category is perfect, given the publishing aims of the software. Good choice!

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Puppyt

Joined: 09 May 2008
Posts: 568
Location: Gatton, Queensland

PostPosted: Sat 07 May 2011, 15:54    Post subject:  

Quick addition to my point '6' above - I just went to
~/Choices/MIME-types
and clicked on "application_pdf" in an attempt to check out the default behaviour. I got the same "Encrypted Document" dialogue as reported earlier - even though no document was in the process of being opened. Hmmmmm. But I still can't see the wood for the trees - will somebody explain this to me or point me to a reference thread in the forum? Getting closer to solving the problem, I feel.
("application_jpeg" tries to open Viewnoir rather than mtPaint. Confused again.)

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Geoffrey


Joined: 30 May 2010
Posts: 1478
Location: Queensland Australia ɹǝpu∩uʍop

PostPosted: Sat 07 May 2011, 18:47    Post subject:  

Puppyt wrote:
Quick addition to my point '6' above - I just went to
~/Choices/MIME-types
and clicked on "application_pdf" in an attempt to check out the default behaviour. I got the same "Encrypted Document" dialogue as reported earlier - even though no document was in the process of being opened. Hmmmmm. But I still can't see the wood for the trees - will somebody explain this to me or point me to a reference thread in the forum? Getting closer to solving the problem, I feel.
("application_jpeg" tries to open Viewnoir rather than mtPaint. Confused again.)


I just had a look at the problem with pdf and tried this, in the " application_pdf" located in ~/Choices/MIME-types

try editing the script to read
Code:
#! /bin/sh
#exec epdfview "$1"
exec epdfview "$@"


that seems to work, don't get the "Encrypted Document" dialogue.

As for " Viewnoir rather than mtPaint " that is determined by defaultimageeditor and defaultimageviewer in /usr/local/bin/

That might give you a clue to fixing your problem.

Geoffrey
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Puppyt

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PostPosted: Sat 07 May 2011, 20:36    Post subject:  

Thanks again Geoffrey,
I tried your script change, and then I changed the default pdf viewer to "PDFedit" (I tried installing "evince" but I think the latest pet is for Puppy 4.3.1 - loads of missing libraries it seems, and no loading. The latest [EDIT] FOXIT READER-lucid pet also failed to install properly). Attempted PDFedit with both "$1" and "$@", and even uninstalled and then re-installed your SciPlore pet. PDFs in SciPlore still reverted to ePDFView and 'encrypted'. But I think that we're on the right track. I'm not happy with my base build and will try another kernel in the 5.2.5 area, I think - with no default PDF viewer present before I install SciPlore, and see how that goes. Just out of interest, what sort of behaviour do you get with different filetypes in your SciPlore mindmaps, if you've tried?
Thanks,
Puppyt

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Geoffrey


Joined: 30 May 2010
Posts: 1478
Location: Queensland Australia ɹǝpu∩uʍop

PostPosted: Sun 08 May 2011, 20:55    Post subject:  

Puppyt,

Ive tried it but I can't get it to view anything, I'm using it in 525

like you said I drag files to it and and create a map but that's about as far as it go's.

when I try clicking on a file to view it I keep getting error box's saying the that it can't find the file at that particular path.

It's got me beat, though it would be good to get it working, after reading about what it does I would find it very useful.

hopefully someone will work out what the problem is, it's beyond me, I'm not that clue'y. Confused

Geoffrey
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Geoffrey


Joined: 30 May 2010
Posts: 1478
Location: Queensland Australia ɹǝpu∩uʍop

PostPosted: Mon 09 May 2011, 02:34    Post subject:  

Puppyt,

I had a look around and came across Compendium, I ran it, looks good, whether its the same but in a different way to SciPlore I really don't know
but it seems to work without fault, I tried it with a pdf , svg not a problem,
it asks you what you want to open them with so it looks a lot easier to set up.

It has video help tutorials and heaps of support by the look of it, it don't look to shabby either, nice GUI would run rings around SciPlore
though it would take a bit of getting use to.

check it out here http://compendium.open.ac.uk/institute/
I downloaded the Compendium 2.0 Beta 1
you just have to give a name and email address to get the download link

seeing that I have it already downloaded I could make a pet.
the pet would be 37meg when extracted it's 77meg
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Puppyt

Joined: 09 May 2008
Posts: 568
Location: Gatton, Queensland

PostPosted: Mon 09 May 2011, 07:24    Post subject:
Subject description: Data management; SciPlore; Compendium
 

Thanks, Geoffrey, for taking the extra time to check that out -
I had a miserable time too with other 5.2 bases, barebone-ish without a default PDF viewer installed. AbiWord still came up trumps as a correctly-linked doc or rtf file/node within SciPlore, but I was getting different "Cannot link" messages for images and pdfs - probably similar path error dialogue as you saw with yours, including some "%" codes and whatnot. My eyes tend to glaze over when I see that sort of gobbledygeek - I didn't take accurate notes at the time. I still dream of getting it working though, perhaps in a fully-fledged pup like LightHouse 5.03, or Bruno (with the Wine option for SciPlore.exe still possible) - or even TEENpup2010minbeta (4.31: http://murga-linux.com/puppy/viewtopic.php?t=52735) - firstly to get it going as Puppy proof-of-principle, and then to work back to what is missing with the linkage structure and where to correct it for a barebones 5.2x. Technological troglodyte that I am, there must be a logic under it even I can understand...(?)
There are still some "official" avenues left for me to try - from SciPlores website:
Quote:
Linux

If you are experiencing difficulties in starting the software you may try running "/lib/freemind.jar". FreeMind's special help page for Linux [http://freemind.sourceforge.net/wiki/index.php/FreeMind_on_Linux] might also be useful for you.

And, I've been on their mailing list for a little over a year now. Perhaps I should ask them directly for hints Smile And another obvious test is to load up the FreeMind pet posted elsewhere on the Puppy forums, and see how that one behaves (but without the pdf specialities of SciPlore).

I really like your suggestion of "Compendium" - though I haven't yet seen any screenies of it, it certainly sounds like a possible alternative and probably something Puppy should have in its software arsenal - even if it isn't open source [Edit: Whups - released under LGPL by UK's Open University] and requires registration. I had a look through some of the reviews and, while a lot of it seems to be self-citing within a clique of technological epistemologists, it certainly seems worth a shot. Yes please - could you make your pet available to the general community, perhaps as a new thread in science/engineering or (better perhaps) Documents?

Many Thanks for all your help - I really appreciate it Smile


PS To all - what I idly dream about is a FireFox add-on to enable dynamic mindmap-type manipulations of Zotero libraries... that would cut out a lot of "middle-apps"

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Puppyt

Joined: 09 May 2008
Posts: 568
Location: Gatton, Queensland

PostPosted: Thu 12 May 2011, 00:13    Post subject:
Subject description: SciPlore in Puppy - is the solution in the java configuration?
 

Just a quick note:-
from http://www.sciplore.org/software/sciplore_mindmapping/manual/en/#Linux:
Quote:

Q: Does SciPlore MindMapping runs under Linux (Ubuntu 9.10)?
A: Some user managed to run the software. We can only encourage you to try (we will publish a special version for Linux soon). One user gave us a brief description how to run SciPlore MindMapping with Ubuntu 9.10:
It also runs fine on Ubuntu Linux 9.10- within the File Browser, I right-clicked on lib/freemind.jar and selected "Open with OpenJDK Java 6 Runtime".

OK so I installed jre-1.3.0.22.pet in dejan555's recent dpup485 puplet and we are talking chalk and cheese regarding the Ubuntu solution (AFAIK), but on reopening SciPlore 15, I now get a new error message when attempting to open PDFs (default to ePDFViewer).
I don't get encryption warnings, just "Error Loading File. Failed to open the PDF file. (mtPaint default gives the same error as before when trying to open a JPG from within SciPlore.)
I think I'm getting a liiiiiittle bit closer to working this out...
But if you are reading this and know the answer, don't just sit there chuckling to yourselves, please Embarassed - Hook in and give me a clue!

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Puppyt

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PostPosted: Thu 12 May 2011, 00:23    Post subject:    

Hmmm if I were a betting man, I'd say that /usr/share/sciplore-15/plugins/svg/pdf-transcoder.jar was partly to blame. Anyone is more than welcome to second the motion and suggest a solution...

[EDIT: Orighty - can't get my jar files 'clickable' (e.g., see http://murga-linux.com/puppy/viewtopic.php?p=30333#30333) despite following the 'Set run action' from within ROX, plus launch script in usr/sbin. In response to "# java -jar pdf-transcoder.jar" run from terminal in the directory listed above, I get a "Failed to load Main-Class manifest attribute from pdf-transcoder.jar" message. Two sides to the same coin, I reckon, but I still could be swinging from the wrong branch in terms of solving PDF access within SciPlore...

NOOBSFLASH: Ok after trawling behind the scenes in the SciPlore directory listed at the top of this post I found that some .jar files were clickable (e.g., Freemind (SciPlore), JabRef2.6, others did nothing (and don't click on the SimplyHTML.jar file - that gives you the flash screen that never dies - across all desktops)). Then I hunted through the SciPloreMindMapping.sh to pick out the possibility that I needed OpenJDK-6-JRE. Downloading now and installing all dependencies, about 80Megs total, from the Debian repositories. Fingers crossed... ]

EDIT: Crying or Very sad

EDIT EDIT: http://murga-linux.com/puppy/viewtopic.php?p=494293#494293 Ariel posted this solution to FreeMind 2 months ago - I'm pinning my hopes that it will also work for it's bigger brother, SciPlore. Idea

EDIT 2 DAYS LATER: Ok Ariel's FreeMind pets and recipe works also in Dpup485, but a re-installed SciPlore (removed first before the FreeMind dependencies were installed, just to be sure) wasn't successful and I got the same responses as posted earlier for images and pdfs. I'm still suspicious of pdf-transcoder.jar but don't have any idea about correcting this issue. I wonder whether the central hassle is related to how Puppy organises its java, and is being pointed to the wrong place i.e., where Debian etc might structure it in under "/usr/java/j2re1.4.2" whatever. Perhaps if the java pet(s) were removed and java reinstalled from the Debian repositories the problem might "go away" for a noob like myself.
No matter - I also tried to run the SciPlore exe under Wine in the same system and couldn't find a way to convince the install that I actually had the required version of java available. Again, it seems that perhaps it was looking in the wrong place for it. Giving up for now, sorry.

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Puppyt

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Location: Gatton, Queensland

PostPosted: Fri 22 Jul 2011, 04:19    Post subject:
Subject description: Skittled SciPlore not a Java issue, but application pointing
 

Cheers All -
revisiting this problem again briefly. I've just tested my previously-described hunch against some recent Puppy builds and ttuuxx's 2.14 remaster project. No joy still on any Puppy5 build with any attempted java recipe, as SciPlore's file linkageing (?) still opens text/doc files seamlessly with AbiWord - but incompletely opens PDF and JPGs with the same results described earlier. ttuuxx's rebuilt-from-scratch 2.14(TOP8) puppy has different behaviour: the docs open fine with his AbiWord, but FireFox is called to open ALL other file types I've placed in a SciPlore mind-map. Therefore it seems apparent (to me, a non-programmer) that as it is installed, SciPlore points its file attributes to incorrect applications/locations in the Puppy file structure.
Barked if I know how to identify and correct this wayward application-calling issue, but it would be well worth solving in the Puppy kennels as the SciPlore team has just been awarded 100 thousand Euros to further their project - so many see value in this application. And, there have already been major improvements since the SciPlore 15beta pet was submitted.

Apologies to any programmer who might be offended by my mixing incorrect terminologies in my update. Please don't let that put you off. Any suggestions in solving this probably simple problem would be most welcome Smile

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ariel


Joined: 03 Jul 2009
Posts: 97

PostPosted: Sat 30 Jul 2011, 09:39    Post subject:  

hi there,

I've got a hack that may help you out. have a look here

do you think I could claim my share of the 100.000? Laughing
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